7UR2

Crystal structure of the Sec14 domain of the RhoGEF Kalirin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	100 mM sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 20-25% PEG3350, 0.2 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.16	α = 81.09
b = 82.42	β = 71.79
c = 83.27	γ = 79.88

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2018-07-09	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-11-16	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-02-15	M	SINGLE WAVELENGTH
4	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2020-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.195	SSRL	BL14-1
2	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9792	SSRL	BL12-2
3	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-2
4	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.89	78.64	95.9	0.061	0.063	0.015	1	31.6	18.3		137673			35.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92	94		1.294	1.329	0.303	0.907	2.2	19

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.89	61.01	137668	6768	95.9	0.196	0.195	0.218	RANDOM	48.49

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.4352	10.4462	-3.061	3.4146	-1.2604	-0.9794

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.46
t_other_torsion	2.8
t_angle_deg	0.99
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.46
t_other_torsion	2.8
t_angle_deg	0.99
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10652
Nucleic Acid Atoms
Solvent Atoms	1412
Heterogen Atoms	35

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.